Admixture-driven genetic diversity supports adaptive potential in Scots pine: Implications for climate-resilient forest management

Climate change poses a significant threat to the sustainability of European forests, emphasizing the urgent need for informed selection of reproductive material and the conservation of genetic resources in key tree species. Scots pine ( Pinus sylvestris L.), one of Europe's most widespread and economically important conifers, exhibits broad phenotypic and ecological variation, making it a priority for adaptive forest management. In this study, we investigated the genetic variation of 56 populations comprising Poland’s best-performing registered seed stands (PL_RSS), ecologically distinct mountain populations (PLM), and reference populations from Northern, Southern, and Western Europe. A total of 1269 individuals were genotyped using mitochondrial DNA markers and over 37,000 genome-wide SNPs to infer demographic history, migration, and potential signatures of historical gene flow. Our analyses revealed high genetic diversity and weak population structure within PL_RSS, consistent with a history of admixture among divergent European lineages, as supported by TreeMix, F-statistics, and spatial migration modelling (FEEMS). In contrast, PLM populations were strongly differentiated, carried unique mt DNA haplotypes, and exhibited signs of long-term isolation, suggesting a glacial refugial origin. These findings provide the first genomic-scale evidence that historical admixture has enhanced the genetic diversity and potential adaptive capacity of Polish Scots pine seed stands. The admixed and genetically rich PL_RSS populations represent valuable resources for breeding programs, including assisted migration and resilience testing under drought and biotic stress conditions. At the same time, the genetically distinct PLM populations warrant conservation priority due to their unique evolutionary legacy. Together, our results advocate a dual forest management strategy combining the use of high-diversity, well-connected seed sources for adaptive forestry with targeted conservation of isolated mountain populations. This approach is essential for preserving genetic diversity, supporting climate-resilient forestry, and maintaining the long-term productivity of Scots pine forests in a rapidly changing environment. • Genome-wide SNP and mtDNA data reveal high diversity in Polish Scots pine seed stands. • Admixture among divergent European lineages enhanced adaptive potential of lowland stands. • Mountain populations show strong differentiation and unique haplotypes of refugial origin. • Dual strategy proposed: conserve isolated mountain stands and utilize admixed seed sources. • Findings support genomics-informed, climate-adaptive forest management in Central Europe.